Magic users are now super powerful, but with the system I'm thinking of they're rare so that makes them easy to pick for a party, but hard to find. They have the fewest class options anyway, short of Yeti's class expansion system. Going purely by vanilla FE7, there's only like what 7 classes unpromoted and promoted each? So make them rare units, but start the player with one mage or whatever so they have a decent magic unit for the beginning of the game.

If you're going to make magic rare enough that all magic users are as or less common than a single physical weapon type, and also all defensively weak, you might as well use a single tome weapon type like modern FE, honestly. It's pretty understandable why IS did it when you think of it that way.